Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome

Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first r...

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Bibliographic Details
Published in:G3: Genes, Genomes, Genetics
Main Authors: Wagner, C Isabel, Kopp, Martina E L, Thorburn, James, Jones, Catherine S, Hoarau, Galice, Noble, Leslie R
Format: Text
Language:English
Published: Oxford University Press 2023
Subjects:
Genome Report
Pacific
spiny dogfish
Squalus acanthias
Online Access:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10468316/
http://www.ncbi.nlm.nih.gov/pubmed/37395764
https://doi.org/10.1093/g3journal/jkad146
Description
Summary:Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first representative of the second largest order of sharks (Squaliformes) with nuclear genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination with Illumina paired-end and Hi-C sequencing, we assembled the genome de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb in size, has a BUSCO completeness score of 91.6%, and an error rate of less than 0.02%. Annotation predicted 33,283 gene models in the spiny dogfish's genome, of which 31,979 are functionally annotated.

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